RegulonDB RegulonDB 10.8: Operon Form
   

sdhCDAB-sucABCD-sdhX operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: sdhCDAB-sucABCD-sdhX
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: sdhCDAB-sucABCD-sdhX
Synonym(s): OP00142, sdhCDAB, sdhCDAB-sucABCD, sucABCD
Gene(s): sdhC, sdhD, sdhA, sdhB, sucA, sucB, sucC, sucD, sdhX   Genome Browser M3D Gene expression COLOMBOS
Note(s): Detection of the full-length sdhCDAB-sucABCD-sdhX transcript, albeit only in rnc and rne mutants, has now established that eight genes encoding three citric acid cycle enzymes are cotranscribed from the sdh promoter. The operon contains one internal promoter (Psuc) and appears to contain two regios of RNAse processing, one located in the sdhB-sucA intergenic region and the other located upstream of sdhX Miyakoshi M,2019. De Mets F,2019.
sdhCDAB, sucAB, and sucCD form a cluster containing two promoters. Transcription of the sucABCD genes is primarily initiated and regulated at the upstream sdh promoter.
Direct evidence for cotranscription of the entire sdhCDAB-sucABCD region from Psdh was obtained by detecting a 10-kb transcript in rnc and rse mutants. sdh and suc genes belong to a single operon.
The absence of a CRP-binding site in the suc promoter region was used to support the early suggestion that the sdh and suc genes are cotranscribed.
Under nitrogen-rich growth conditions, the expression of the sdhC gene increased in mutants for two genes that encode two terminal oxidases, cyoA and cydB, and in mutants for two transcriptional regulators, Fnr and Fur. However, under nitrogen-limited growth conditions, gene expression was decreased Kumar R,2011.
The expression of this operon is enhanced during and after the switch from aerobic to anaerobic growth conditions 21980479.
The expression of the gene sdhC is decreased under acidic growth conditions in either aerobiosis or microaerobiosis Marzan LW,2013.
DcuR appears to affect the expression of sdhC in response to fumarate; however, no site to bind DcuR was located around the sdhCp promoter Surmann K,2020.

In a study where it was shown that the L-tryptophan eradicated persister cells, it was observed that the exogenous amino acid decreased the expression of the sucA and sdhD genes 31271063.
Based on DNA microarray analysis, the mechanism of bacterial inactivation by carvacrol and citral was studied 28644990. Treatment by both compounds caused membrane damage and activated metabolism through the production of nucleotides required for DNA and RNA synthesis and metabolic processes 28644990. A total of 76 and 156 genes demonstrated significant transcriptional differences by carvacrol and citral, respectively. Genes upregulated by carvacrol treatment included the multidrug efflux pump genes acrA and mdtM, genes related to the phage shock response, pspA, pspB, pspC, pspD, pspF, and pspG, and genes whose products are important for biosynthesis of arginine (argC, argG, artJ) and purine nucleotides (purC, purM). Genes upregulated by citral treatment included purH, pyrB, and pyrI. On the other hand, mutations in several differentially expressed genes confirmed the roles of ygaV, yjbO, pspC, sdhA, yejG, and ygaV in mechanisms of inactivation by carvacrol and citral 28644990.
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [1] Cunningham L., et al., 1998
[2] Magnusson K., et al., 1986
[3] Wood D., et al., 1984
Promoter
Name: sdhCp
+1: 754958
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 219
Sequence: cgacaaactatatgtaggttaattgtaatgattttgtgaacagcctatactgccgccaggTctccggaacaccctgcaatc
                       -35                    -10           +1                   
Evidence: [HIPP]
[TIM]
Reference(s): [4] Wilde RJ., et al., 1986
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote ArcA-Phosphorylated activator sdhCp 754740 754754 -211.0 tgttacataaGTTAATCTTAGGTGAaataccgact nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [5]
remote ArcA-Phosphorylated activator sdhCp 754814 754828 -137.0 ttgtaacaacTTTGTTGAATGATTGtcaaattaga nd [BPP], [GEA] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ArcA-Phosphorylated repressor sdhCp 754919 754933 -32.0 atgtaggttaATTGTAATGATTTTGtgaacagcct nd [APIORCISFBSCS], [BPP], [CV(CHIP-SV/GEA/ROMA)], [CV(GEA/ROMA)], [GEA] [6], [12]
proximal ArcA-Phosphorylated repressor sdhCp 754924 754938 -27.0 ggttaattgtAATGATTTTGTGAACagcctatact nd [APIORCISFBSCS], [CV(GEA/ROMA)], [GEA] [1], [5], [12], [13]
remote ArcA-Phosphorylated repressor sdhCp 755207 755221 257.0 acaaagacctGTTAATCTGGACCTAcagaccatcc nd [BPP], [GEA] [5]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP1 activator sdhCp 754864 754886 -83.5 taaatgttgtTATCGTGACCTGGATCACTGTTCaggataaaac nd [AIBSCS], [BCE], [CV(GEA/ROMA)], [GEA] [1], [4], [6], [7], [8], [9], [10]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR repressor sdhCp nd nd nd nd nd [GEA] [11], [13]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ activator sdhCp 754915 754933 -34.0 ctatatgtagGTTAATTGTAATGATTTTGtgaacagcct nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [9], [11]
Note(s): 1Early work with an sdh-galk fusion indicates that crp and cya are required for maximum expression, and S1 mapping studies not only confirmed that sdh transcription is severely repressed by glucose but indicated that there is a potential CRP-binding site at -80 in the sdh promoter region.
This promoter and its CRP-binding site are responsible for the coordinate expression and the glucose-mediated repression of ODH and SCS synthesis.3Early work with an sdh-galk fusion indicates that crp and cya are required for maximum expression, and S1 mapping studies not only confirmed that sdh transcription is severely repressed by glucose but indicated that there is a potential CRP-binding site at -80 in the sdh promoter region.
This promoter and its CRP-binding site are responsible for the coordinate expression and the glucose-mediated repression of ODH and SCS synthesis.


Transcription unit          
Name: sdhDAB
Gene(s): sdhD, sdhA, sdhB   Genome Browser M3D Gene expression COLOMBOS
Note(s): A transcript that contains sdhA and sdhB is decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [14] Spencer ME., et al., 1985
[4] Wilde RJ., et al., 1986
Promoter
Name: sdhDp2
+1: 755404
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 156
Sequence: aggtttcgagcaagcttccgcgattatgggcagcttcttcgtcaaatttatcatgtggggCatccttaccgctctggcgta
                        -35                      -10        +1                   
Note(s): The sdh promoters generate two polycistronic mRNAs, a long 3,493-base sdhCDAB transcript (p1) and a shorter 3,047-base sdhDAB transcript (p2). sdhDAB (major), 1,455 bp upstream of sdhD (i.e., within sdhC) TGGGCA/16bp/TATCAT (P2 positions 1284-1311) sdhDp 156 bp upstream from the sdhD gene TGGGCA/16bp/TATCAT 7 bp upstream. Note that the operation of alternative σ-type promoters cannot be ruled out.
Evidence: [HIPP]
[TIM]
Reference(s): [4] Wilde RJ., et al., 1986
Terminator(s)
Type: rho-dependent
Sequence: tcgcatcaggCAACCAGtgccggatgc
Reference(s): [14] Spencer ME., et al., 1985
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator sdhDp2 755380 755401 -13.0 tgggcagcttCTTCGTCAAATTTATCATGTGGggcatcctta nd [BCE] [4]


Transcription unit          
Name: sucAB
Gene(s): sucA, sucB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Cunningham L., et al., 1998
[14] Spencer ME., et al., 1985
Promoter
Name: sucAp
+1: 758586
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 120
Sequence: cgtaacaaagaaatgcaggaaatctttaaaaactgcccctgacactaagacagtttttaaAggttccttcgcgagccacta
                         -35             -10                +1                   
Note(s): There is a single suc promoter upstream of the sucA gene, and transcription continues between the sucAB and sucCD genes; no independent transcription of the sucCD genes has been detected.
Expression from the suc promoter was partially activated by σ38.
sucAp appears to be repressed by CRP, although no CRP site has been found. The significance of this 2-fold repression is obscure.
Evidence: [TIM]
Reference(s): [1] Cunningham L., et al., 1998
[14] Spencer ME., et al., 1985
Terminator(s)
Type: rho-dependent
Sequence: aagcgatacgAAATATTCggtctacggt
Reference(s): [14] Spencer ME., et al., 1985
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated repressor sucAp nd nd nd nd nd [BPP], [GEA] [6], [15], [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR repressor sucAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6], [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd IHF1 repressor sucAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [1], [6]
Note(s): 1Expression from the suc promoter was repressed by IHF. The consequences of inactivating other potential regulators showed that IHF performs a major role in repressing the suc promoter may be initiated by σ38.3Expression from the suc promoter was repressed by IHF. The consequences of inactivating other potential regulators showed that IHF performs a major role in repressing the suc promoter may be initiated by σ38.


Transcription unit          
Name: sucABCD
Synonym(s): OP00143, suc
Gene(s): sucA, sucB, sucC, sucD   Genome Browser M3D Gene expression COLOMBOS
Note(s): The sucAB genes are flanked by three and four REP sequences.
ArcA appears to repress sucD gene expression under anaerobiosis. Two putative ArcA binding sites were identified 69, 267 and 330 bp upstream of this gene Salmon KA,2005, but no promoter upstream of it has been identified. Instead, sucD is transcribed from two promoters one of them is located usptream of sdhC gene and the other one upstream of sucA gene. The sdhCp promoter is repressed by ArcA.
Disruption of the sucA and sucB genes notably decrease survival under high hydrostatic pressure (HHP). On the other hand, disruption of the sucC and sucD genes increase resistance to high hydrostatic pressure (HHP). This disruption was mediated by increased basal RpoS activity levels, although the activity levels did not correlate with the changes in heat resistance 30497599 TCA cycle enzymes can profoundly affect HHP resistance 30497599
Evidence: [LTED] Length of transcript experimentally determined
Reference(s): [17] Buck D., et al., 1989
[18] Buck D., et al., 1986
[1] Cunningham L., et al., 1998
Promoter
Name: sucAp
+1: 758586
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 120
Sequence: cgtaacaaagaaatgcaggaaatctttaaaaactgcccctgacactaagacagtttttaaAggttccttcgcgagccacta
                         -35             -10                +1                   
Note(s): There is a single suc promoter upstream of the sucA gene, and transcription continues between the sucAB and sucCD genes; no independent transcription of the sucCD genes has been detected.
Expression from the suc promoter was partially activated by σ38.
sucAp appears to be repressed by CRP, although no CRP site has been found. The significance of this 2-fold repression is obscure.
Evidence: [TIM]
Reference(s): [1] Cunningham L., et al., 1998
[14] Spencer ME., et al., 1985
TF binding sites (TFBSs)
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ArcA-Phosphorylated repressor sucAp nd nd nd nd nd [BPP], [GEA] [6], [15], [16]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd FNR repressor sucAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [6], [15]
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd IHF1 repressor sucAp nd nd nd nd nd [AIBSCS], [CV(GEA/ROMA)], [GEA] [1], [6]
Note(s): 1Expression from the suc promoter was repressed by IHF. The consequences of inactivating other potential regulators showed that IHF performs a major role in repressing the suc promoter may be initiated by σ38.3Expression from the suc promoter was repressed by IHF. The consequences of inactivating other potential regulators showed that IHF performs a major role in repressing the suc promoter may be initiated by σ38.


Regulation by sRNA    
  Small RNA name (Regulator) Regulation type Mechanism Function Binding Sites Evidence Reference
LeftPos RightPos Sequence (RNA-strand)
  ryhB antisense post-transcriptional regulation repressor       [GEA]
[HIFS]
[IMP]
[19]
Notes: "The provided sequence is that of the RNA strand,i.e. 'U's are showed instead the 'T'"




Reference(s)    

 [1] Cunningham L., Guest JR., 1998, Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli., Microbiology 144 ( Pt 8):2113-23

 [2] Magnusson K., Philips MK., Guest JR., Rutberg L., 1986, Nucleotide sequence of the gene for cytochrome b558 of the Bacillus subtilis succinate dehydrogenase complex., J Bacteriol 166(3):1067-71

 [3] Wood D., Darlison MG., Wilde RJ., Guest JR., 1984, Nucleotide sequence encoding the flavoprotein and hydrophobic subunits of the succinate dehydrogenase of Escherichia coli., Biochem J 222(2):519-34

 [4] Wilde RJ., Guest JR., 1986, Transcript analysis of the citrate synthase and succinate dehydrogenase genes of Escherichia coli K12., J Gen Microbiol 132(12):3239-51

 [5] Shen J., Gunsalus RP., 1997, Role of multiple ArcA recognition sites in anaerobic regulation of succinate dehydrogenase (sdhCDAB) gene expression in Escherichia coli., Mol Microbiol 26(2):223-36

 [6] Lynch AS., Lin EC., 1996, Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promoters., J Bacteriol 178(21):6238-49

 [7] Surmann K., Stopp M., Worner S., Dhople VM., Volker U., Unden G., Hammer E., 2020, Fumarate dependent protein composition under aerobic and anaerobic growth conditions in Escherichia coli., J Proteomics 212:103583

 [8] Tsai MJ., Wang JR., Yang CD., Kao KC., Huang WL., Huang HY., Tseng CP., Huang HD., Ho SY., 2018, PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli., Sci Rep 8(1):951

 [9] Zhang Z., Gosset G., Barabote R., Gonzalez CS., Cuevas WA., Saier MH., 2005, Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli., J Bacteriol 187(3):980-90

 [10] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [11] Kumar R., Shimizu K., 2011, Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures., Microb Cell Fact 10:3

 [12] Iuchi S., Lin EC., 1988, arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways., Proc Natl Acad Sci U S A 85(6):1888-92

 [13] Park SJ., Tseng CP., Gunsalus RP., 1995, Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: role of ArcA and Fnr., Mol Microbiol 15(3):473-82

 [14] Spencer ME., Guest JR., 1985, Transcription analysis of the sucAB, aceEF and lpd genes of Escherichia coli., Mol Gen Genet 200(1):145-54

 [15] Park SJ., Chao G., Gunsalus RP., 1997, Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter., J Bacteriol 179(13):4138-42

 [16] Spiro S., Guest JR., 1991, Adaptive responses to oxygen limitation in Escherichia coli., Trends Biochem Sci 16(8):310-4

 [17] Buck D., Guest JR., 1989, Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon., Biochem J 260(3):737-47

 [18] Buck D., Spencer ME., Guest JR., 1986, Cloning and expression of the succinyl-CoA synthetase genes of Escherichia coli K12., J Gen Microbiol 132(6):1753-62

 [19] Masse E., Gottesman S., 2002, A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli., Proc Natl Acad Sci U S A 99(7):4620-5


RegulonDB